[2024-01-24 12:40:20,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5e0e2b7-85cf-4618-b62c-59a075b24465/dqc_reference
[2024-01-24 12:40:22,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:22,106] [INFO] Task started: Prodigal
[2024-01-24 12:40:22,106] [INFO] Running command: gunzip -c /var/lib/cwl/stgf676ec05-59cb-4584-b296-0a6120576c56/GCF_000253235.1_ASM25323v1_genomic.fna.gz | prodigal -d GCF_000253235.1_ASM25323v1_genomic.fna/cds.fna -a GCF_000253235.1_ASM25323v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:43,500] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:43,501] [INFO] Task started: HMMsearch
[2024-01-24 12:40:43,501] [INFO] Running command: hmmsearch --tblout GCF_000253235.1_ASM25323v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5e0e2b7-85cf-4618-b62c-59a075b24465/dqc_reference/reference_markers.hmm GCF_000253235.1_ASM25323v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:43,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:43,840] [INFO] Found 6/6 markers.
[2024-01-24 12:40:43,906] [INFO] Query marker FASTA was written to GCF_000253235.1_ASM25323v1_genomic.fna/markers.fasta
[2024-01-24 12:40:43,907] [INFO] Task started: Blastn
[2024-01-24 12:40:43,907] [INFO] Running command: blastn -query GCF_000253235.1_ASM25323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5e0e2b7-85cf-4618-b62c-59a075b24465/dqc_reference/reference_markers.fasta -out GCF_000253235.1_ASM25323v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:45,195] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:45,199] [INFO] Selected 13 target genomes.
[2024-01-24 12:40:45,199] [INFO] Target genome list was writen to GCF_000253235.1_ASM25323v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:45,205] [INFO] Task started: fastANI
[2024-01-24 12:40:45,205] [INFO] Running command: fastANI --query /var/lib/cwl/stgf676ec05-59cb-4584-b296-0a6120576c56/GCF_000253235.1_ASM25323v1_genomic.fna.gz --refList GCF_000253235.1_ASM25323v1_genomic.fna/target_genomes.txt --output GCF_000253235.1_ASM25323v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:41:13,156] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:13,157] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5e0e2b7-85cf-4618-b62c-59a075b24465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:41:13,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5e0e2b7-85cf-4618-b62c-59a075b24465/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:41:13,179] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:41:13,179] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:41:13,179] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Streptomyces venezuelae	strain=ATCC 10712	GCA_000253235.1	54571	54571	type	True	99.9997	2740	2742	95	conclusive
Streptomyces venezuelae	strain=ATCC 10712	GCA_008639165.1	54571	54571	type	True	99.9744	2728	2742	95	conclusive
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	99.584	2005	2742	95	conclusive
Streptomyces zaomyceticus	strain=JCM 4864	GCA_014656215.1	68286	68286	type	True	90.8542	2058	2742	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	90.166	1963	2742	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	90.12	1978	2742	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.7358	2053	2742	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.714	2019	2742	95	below_threshold
Streptomyces litmocidini	strain=JCM 4394	GCA_014649755.1	67318	67318	type	True	89.2764	1932	2742	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.2315	1982	2742	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	82.9576	1526	2742	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.7212	1398	2742	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.3593	1308	2742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:41:13,181] [INFO] DFAST Taxonomy check result was written to GCF_000253235.1_ASM25323v1_genomic.fna/tc_result.tsv
[2024-01-24 12:41:13,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:41:13,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:41:13,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5e0e2b7-85cf-4618-b62c-59a075b24465/dqc_reference/checkm_data
[2024-01-24 12:41:13,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:41:13,253] [INFO] Task started: CheckM
[2024-01-24 12:41:13,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000253235.1_ASM25323v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000253235.1_ASM25323v1_genomic.fna/checkm_input GCF_000253235.1_ASM25323v1_genomic.fna/checkm_result
[2024-01-24 12:43:17,628] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:17,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:17,662] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:17,662] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:17,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000253235.1_ASM25323v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:17,663] [INFO] Task started: Blastn
[2024-01-24 12:43:17,663] [INFO] Running command: blastn -query GCF_000253235.1_ASM25323v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd5e0e2b7-85cf-4618-b62c-59a075b24465/dqc_reference/reference_markers_gtdb.fasta -out GCF_000253235.1_ASM25323v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:19,787] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:19,791] [INFO] Selected 11 target genomes.
[2024-01-24 12:43:19,791] [INFO] Target genome list was writen to GCF_000253235.1_ASM25323v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:19,868] [INFO] Task started: fastANI
[2024-01-24 12:43:19,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgf676ec05-59cb-4584-b296-0a6120576c56/GCF_000253235.1_ASM25323v1_genomic.fna.gz --refList GCF_000253235.1_ASM25323v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000253235.1_ASM25323v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:44,088] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:44,104] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:44,104] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_008639165.1	s__Streptomyces venezuelae	99.9744	2728	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	conclusive
GCF_001418135.1	s__Streptomyces aureus_A	91.2719	1784	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_000717595.1	s__Streptomyces flavochromogenes	91.2072	2187	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5951	N/A	N/A	N/A	N/A	1	-
GCF_014451325.1	s__Streptomyces sp014451325	91.1137	1445	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905825.1	s__Streptomyces sp001905825	90.9779	2151	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
GCF_014656215.1	s__Streptomyces zaomyceticus	90.8174	2063	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426405.1	s__Streptomyces sp001426405	90.2777	1998	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001905665.1	s__Streptomyces sp001905665	90.1113	1973	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042145.1	s__Streptomyces sp008042145	90.0789	1933	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.721	2055	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_003386135.1	s__Streptomyces sp003386135	89.2426	2020	2742	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:43:44,106] [INFO] GTDB search result was written to GCF_000253235.1_ASM25323v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:44,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:44,109] [INFO] DFAST_QC result json was written to GCF_000253235.1_ASM25323v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:44,109] [INFO] DFAST_QC completed!
[2024-01-24 12:43:44,110] [INFO] Total running time: 0h3m23s